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No, the everstone works. I'm not quite sure what your problem is other than perhaps really bad luck.

I end up with one adamant nature cleffa out of 15 offspring. I decided to switch out my male Clefairy I was breeding for a female Clefairy and out of the four eggs I have since hatched, three had an adamant nature.

I have a ditto with an adamant nature with an everstone in the daycare along with a clefairy. Yet so far, I have gotten 12 cleffa, none of which have an adamant nature.

The odds of that happening are 1 in 4096, which leads me to believe that the everstone no longer works?

Did one of your parents originate in another country's version of B/W?

If so, there's your answer. If that foreign parent is the clefairy, rather than breeding the foreign parent clefairy, breed the resulting Cleffa(after it evolves into Clefairy, since Cleffa can't breed with anyone) with that same Ditto instead. However, if the foreign parent is the Ditto, then tough luck: you'll be forced to catch either an Adamant ditto from the same region as the clefairy, or vice versa, as you can't breed to get a baby Ditto, meaning no adamant cleffa until you breed a clefairy from the same region as the ditto/breed an adamant ditto from the same region as the clefairy while that same ditto holds the everstone...

Did one of your parents originate in another country's version of B/W?

If so, there's your answer. If that foreign parent is the clefairy, rather than breeding the foreign parent clefairy, breed the resulting Cleffa(after it evolves into Clefairy, since Cleffa can't breed with anyone) with that same Ditto instead. However, if the foreign parent is the Ditto, then tough luck: you'll be forced to catch either an Adamant ditto from the same region as the clefairy, or vice versa, as you can't breed to get a baby Ditto, meaning no adamant cleffa until you breed a clefairy from the same region as the ditto/breed an adamant ditto from the same region as the clefairy while that same ditto holds the everstone...

Actually, this is no longer true in B/W. My many modest Masuda-method made Vanillite can attest to that.

"We didn't want to go, we didn't want to kill them, but its persistent silence and outstretched arms horrified and comforted us at the same time..."||

For some reason, either my national dex isn't showing up, or I can't figure out how to switch from the Unova dex to the national dex. I already beat enough of the game for the credits to roll, and I returned to my hometown. It said my dex was upgraded, yet I can't seem to figure out how to look at the national dex part, only the Unova dex. Is there something I missed?

100% of information in signatures on this forum involving percentages is false. If you feel as cheated by this atrocity as I do, don't you dare copy this into your signature.
Hold on... if this percentage was correct at the time of print, that means the actual percentage of false information is less than 100% if this signature is included. Which means that... no! I've become a slave to the system!!

I've given my Eevee Pokerus to help with EV training, and all of a sudden, in the middle of training, it's gone (which now makes my task that much more difficult). It now has the little frowning face in its summary. Is it possible to re-infect it with Pokerus, or is it a one time deal? I've tryed and it hasn't seemed to work so I was curious if there's another way.

I've given my Eevee Pokerus to help with EV training, and all of a sudden, in the middle of training, it's gone (which now makes my task that much more difficult). It now has the little frowning face in its summary. Is it possible to re-infect it with Pokerus, or is it a one time deal? I've tryed and it hasn't seemed to work so I was curious if there's another way.

Thanks.

Pokerus is still in effect, it just can't inflict it on other pokemon now.

for the battle subway, for the wifi train, is it possible to team up with someone over wifi, or is it just yourself vs random people over wifi. cuz on serebii it says tag team with a friend over wifi, but in the game it gives no option for it? or am i doing something wrong?

Did anyone ever figure out if the Zekrom/Resiram from Dragon Spiral Tower can be shiny? I was bored and decided to spend most of my free time in the last week filling up my boxes for this, and I finally did it yesterday. So now that I can catch Zekrom in Dragon Spiral Tower, did anyone ever find out for sure if it can be shiny or not there? And I don't want any "I think..." answers, I want to know if anyone has any facts on it.

Did anyone ever figure out if the Zekrom/Resiram from Dragon Spiral Tower can be shiny? I was bored and decided to spend most of my free time in the last week filling up my boxes for this, and I finally did it yesterday. So now that I can catch Zekrom in Dragon Spiral Tower, did anyone ever find out for sure if it can be shiny or not there? And I don't want any "I think..." answers, I want to know if anyone has any facts on it.

No, even though gamefreak have produced shiny sprites for reshiram and zekrom, there's no way that you can catch one shiny in game. I imagine you could get one through hacking/ game shark, but who really wants to do that?